I haven't seen any of this myself, so it's hard to know whether your issue is related or just similar. One way or another, it might be in your interest to start a support ticket with Toodledo so you can provide more detail, and maybe even screenshots of what you are seeing.

If you edit a note, and then click outside of the note to cause it to save, and then immediately re-edit the note before it has had a chance to finish saving, it is possible for the carriage returns to be removed. We will fix this in the next update, but in the meantime, when you save a note, wait for the orange spinner to go away before re-editing it.